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Furthermore, it has been shown that microsatellites are enriched at breakpoints of SDs suggesting the possible role of microsatellite repeats in the genesis of SDs [ 20].

Furthermore, since microsatellites are enriched in both hot IGRs and hot ORFs as defined by the DSB map by Gerton et al., [ 42], and recombination breakpoints mapped on the finest possible scale are concentrated almost entirely in IGRs in yeast [ 55], the relationship between microsatellites and recombination probably is distal to some degree.

Methods and Results: Microsatellite loci were enriched in a genomic sample and isolated using pyrosequencing.

The PCR was performed on a PTC-100 PCR machine with the following program: 20 cycles of 95°C for 8 s, 68°C for 20 s and 72°C for 3 min. Microsatellites in cDNA were enriched by using biotinylated oligonucleotides and streptavidin-coated magnetic beads.

Next, using functions in the R package 'GOstats' (Falcon and Gentleman 2007), we investigated whether the mature microsatellite-containing genes were enriched for specific GO functional annotations (in comparison to the genes in the remainder of the genome).

Additionally, size-selected fragments from genomic DNA were enriched for microsatellites by Ecogenics GmbH (Zürich-Schlieren, Switzerland) using streptavidin-coated magnetic beads and biotin-labeled (CT 13 and (GT 13 repeat probes.

Digested, ligated DNA fragments were enriched for microsatellites by hybridization to 3′-biotinylated oligonucleotide repeat probes (GT 8 (i.e., GTGTGTGTGTGTGTGT), (TC 9.5, (GTT 6.33, (TTC 7, (GTA 8.33, (GTG 4.67, (TCC 5, (TTTG 2.5, (TTTC 6, (TTAC 6.75, and (GATG 4.25 (Integrated DNA Technologies).

Size-selected genomic DNA fragments were enriched for microsatellite content by using magnetic streptavidin beads and biotin-labeled GATA, GTAT, AAAC, and AAAG repeat oligonucleotides.

The amplified fragments (200 800 bp) were enriched for microsatellite repeats by magnetic bead selection with 5′-biotinylated (AC 15, (AG 15, and (AAG 10 probes.

Genomic DNA was digested with RsaI enzyme (Invitrogen, Carlsbad, California, USA) for 3 h incubation at 37°C, and the digested fragments were enriched in microsatellite fragments using (CT 8 and (GT 8 motifs.

CA- and GA-microsatellites located in the 300 BAC clones were enriched according to a previous protocol [ 24] with some modifications [ 25].